tbuckley/cabot-search huggingface dataset:
Abstract 998: Extracellular proximity labeling (ePL) as a tool to identify protein-protein interactions in the tumor microenvironment
Authors: Sadeechya Gurung
Journal: Cancer Research (2022)

Abstract The extracellular matrix (ECM) is a dynamic niche that is extensively reshaped in the development of the tumor microenvironment (TME). Our current understanding of ECM function and dynamics is largely informed by identification of protein-protein interactions (PPIs) using co-immunoprecipitation (co-IP) techniques that may miss transient and weak/unstable interactions. Recent advances in proximity labeling techniques have greatly expanded the interactome networks of numerous intracellular proteins, however these tools have yet to be extended to study PPIs in the ECM. We have recently optimized a systematic approach to identify PPIs in the ECM using fusion constructs of the biotinylating enzymes, BioID2 and TurboID, with the widely expressed matrix regulator TIMP2. BioID2 and TurboID offer differing reaction kinetics that may provide complimentary information on extracellular PPIs (ePPIs). Matrix metalloproteinases (MMPs) and their endogenous inhibitors, tissue inhibitors of metalloproteinases (TIMPs) are crucial regulators of ECM structure and composition. TIMPs are widely expressed multifunctional proteins that serve to promote ECM homeostasis that is often perturbed in many cancers and chronic disorders. Although biochemical data suggests that TIMPs are promiscuous proteins, the TIMP interactome is poorly defined. We have optimized a protocol for the identification of ePPIs for the TIMP family of proteins. Fusion constructs equipped with a promiscuous biotin ligase (BioID2/TurboID) fused to the N- or C-terminal of full length TIMP2 were packaged into retroviral vectors for cellular delivery. Cells were exposed to the extracellular proximity labelling (ePL) fusion proteins and processed in our optimized analysis pipeline. ePPIs were identified via streptavidin pulldown and proteomic techniques. We present our optimized ePL pipeline and show that this technique is an effective tool for the identification of novel ePPIs for multiple extracellular targets. Citation Format: Sadeechya Gurung. Extracellular proximity labeling (ePL) as a tool to identify protein-protein interactions in the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 998.
Abstract 5841: Discovery of a novel epigenetic regulatory axis that mediates sorafenib's antineoplastic activity
Authors: Tianzi Wei, Hao Wang, Risheng Lin, Yueming Li, Yi Lu, Jian Zhang
Journal: Cancer Research (2022)

Abstract As a multi-kinase inhibitor, sorafenib has been widely used to treat advanced hepatocellular carcinoma patients since 2007. Sorafenib, however, is associated with severe drug adverse effects and drug resistance. Therefore, the strategies to improve the antineoplastic effects of sorafenib are urgently needed. In this study, we observed that metallothionein-1G (MT1G), was significantly activated by sorafenib and mediated sorafenib’s antineoplastic activity both in vitro and in vivo. Our study also proved that sorafenib effectively inhibited the activity of several critical enzymes required for maintaining methylation level in hepatoma cells to activate MT1G. In addition, the ATAC-seq results demonstrated that the promotor region of MT1G become more accessible upon the treatment of sorafenib, which may make a few key transcription factors easier to bind to the promoter region of MT1G to initiate the transcription. Finally, next-generation sequencing (NGS) results showed that the expression of two tumor associated genes: KLF4 and CA9, were significantly altered by MT1G overexpression. KLF4 was required to bind to the promotor region of CA9 and then inhibit the expression of CA9, a hypoxia-induced gene involved in modulating tumor microenvironment. The decrement of CA9 expression was related to hepatoma cells suppression. Taken together, we deduce that MT1G-KLF4-CA9 axis is a potential novel pathway to suppress hepatoma cell progression regulated by sorafenib. The regulation of MT1G-KLF4-CA9 is plausible to synergize with sorafenib to improve the therapeutic effects. Supported by NSFC projects 81773146, 81972766, 81972420, 82173336; Shenzhen Science and Technology Commission Project JCYJ20180302174235893; Sanming Project of Medicine in Shenzhen SZSM202003009; Guangdong Basic and Applied Basic Research Foundation 2021A1515012161; and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research (2017B030301018) Citation Format: Tianzi Wei, Hao Wang, Risheng Lin, Yueming Li, Yi Lu, Jian Zhang. Discovery of a novel epigenetic regulatory axis that mediates sorafenib's antineoplastic activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5841.
Abstract 976: Interrogating the pre-metastastic gene signature to block brain metastases
Authors: Agata Kieliszek, Blessing Bassey-Archibong, Chitra Venugopal, Sheila Singh
Journal: Cancer Research (2022)

Abstract BACKGROUND: The incidence of brain metastases (BM) is tenfold higher than that of primary brain tumors. BM predominantly originate from primary lung, breast, and melanoma tumors with a 90% mortality rate within one year of diagnosis, posing a large unmet clinical need to identify novel therapies against BM. The goal of this work is to uncover the molecular factors that drive the formation of BM and investigate whether we can slow down and ultimately block BM formation. METHODS: The Singh lab has generated a large in-house biobank of patient-derived BM cell lines that are established from BM patient tumor samples. We use these BM cell lines to generate murine orthotopic xenograft models of BM and interrogate the biological processes that lead to BM. These models have successfully recapitulated all the stages of their respective BM cascades and additionally captured a “pre-metastatic” population of BM cells that have just seeded the brains of mice before forming mature, clinically detectable tumors. Pre-metastatic cell populations are impossible to detect in human patients but represent a therapeutic window wherein metastasizing cells can be targeted and eradicated before establishing clinically detectable and difficult to treat brain tumors. RESULTS: RNA sequencing of pre-metastatic BM cells revealed a unique deregulated transcriptomic profile that is specific to pre-metastatic cells despite the tumor of origin. Subsequent Connectivity Map analysis revealed compounds that we biologically characterized in vitro for selective anti-BMIC phenotypes. This effort led to a lead compound that exhibits anti-BM activity in vitro, while remaining ineffective against normal brain cell controls. Preliminary in vivo work has shown that following both orthotopic and intracardiac injection of BM cells, treatment with this lead compound reduces the tumor burden compared to mice being treated by a vehicle control, while providing a significant survival advantage. Ongoing mechanistic investigations aim to delineate the protein target of this compound in the context of the observed selective anti-BM phenotype. CONCLUSION: Identification of novel small molecules that target premetastatic BM cells could slow or prevent the formation of BM and dramatically improve the prognosis of at-risk cancer patients. Citation Format: Agata Kieliszek, Blessing Bassey-Archibong, Chitra Venugopal, Sheila Singh. Interrogating the pre-metastastic gene signature to block brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 976.
Abstract 6223: PD3D®models: New age in cancer research and clinical diagnostics
Authors: Alina Pflaume, Samantha Exner, Katja Herrera-Glomm, Jürgen Loskutov, Ulrike Pfohl, Manuela Regenbrecht, Sushmitha Sankarasubramanian, Lena Wedeken, Sabine Finkler, Larissa Ruhe, Quirin Graf Adelmann, Christoph Reinhard, Philipp Stroebel, Christian R. Regenbrecht
Journal: Cancer Research (2022)

Abstract Patient-derived 3D cell culture models (PD3D®) developed as a powerful tool for disease modelling, biomarker and drug discovery. Currently, they are gaining increasing significance in the field of personalized oncology, as they recapitulate the histopathology of the original tumor tissue and preserve its genetic markup. PD3D® can be used to model intratumoral heterogeneity and for medium and high throughput drug screens. Using a reverse clinical engineering approach, PD3D® models allow identification of chemoresistance/sensitivity signatures (i.e., biomarkers) and can be applied in personalized oncology to identify treatment for an individual patient. We successfully established PD3D® models from more than 300 tumor tissue samples, ranging from more prevalent cancers like colorectal, breast and pancreas carcinoma, to rare tumor entities including various sarcoma types and thymoma. PD3D® models from different tumor entities differ in morphology and culture media requirements. When treating PD3D® from the same tumor entity with standard of care drugs, we found that their response differed, as does clinical response of patients. Furthermore, we successfully used PD3D® models to identify a biomarker for predicting chemosensitivity towards a targeted drug. For application of PD3D® in truly personalized oncology, we developed a protocol that allows us to generate a PD3D® culture and perform a drug sensitivity assay for an individual patient within a therapy-relevant timeframe. Using this protocol, we identified a combination therapy for a pretreated, metastasized appendix carcinoma within 29 days, that resulted in stable disease of the patient. In conclusion, PD3D® models can be derived from various cancer entities and used to analyze drug response in cohorts of models for drug development or identification of signatures related to drug resistance or sensitivity. Furthermore, PD3D® models can be used to predict a patient tumor’s drug response in a personalized manner, supporting the oncologist to identify the best treatment option for the patient. Citation Format: Alina Pflaume, Samantha Exner, Katja Herrera-Glomm, Jürgen Loskutov, Ulrike Pfohl, Manuela Regenbrecht, Sushmitha Sankarasubramanian, Lena Wedeken, Sabine Finkler, Larissa Ruhe, Quirin Graf Adelmann, Christoph Reinhard, Philipp Stroebel, Christian R. Regenbrecht. PD3D®models: New age in cancer research and clinical diagnostics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6223.
Abstract 1084: FlexBodies: Targeting intracellular tumor antigens with T cell redirecting bispecific antibodies
Authors: Lauric Haber, ryan McKay, jennifer Finney, stephen castaneda, kristen spitler, sahar Rizvi, aidan Hwang, kevin Bray, willy Ramos, pamela Krueger, frank delfino, Craig Meagher, tammy huang, yang shen, william olson, john Lin, eric smith
Journal: Cancer Research (2022)

Abstract Bispecific antibodies engineered to recruit T cells as a means to kill tumor cells are a promising new class of therapeutics in the field of oncology. A challenge for this class of agents is the requirement for cell surface expressed tumor specific targets, as a large number of tumor-specific antigens are only expressed intracellularly. One strategy to access these targets is to take advantage of the natural processing and presentation of intracellular antigens in the context of the major histocompatibility complex (MHC). However, this requires the development of therapeutics that can be active against targets with a very low surface density. Here, we describe the generation and characterization of Flexbodies, a novel format bispecific antibody engineered to target MHC-peptide tumor neoantigens. We demonstrate that the orientation of the targeting arms and the valency of these reagents allow specific T-cell activation and potent cytotoxic activity against cell lines expressing endogenous level of peptide antigens. This bispecific format has the potential to become an important new tool to expand the range of tumors able to be specifically targeted with t-cell redirecting biologics. Citation Format: Lauric Haber, ryan McKay, jennifer Finney, stephen castaneda, kristen spitler, sahar Rizvi, aidan Hwang, kevin Bray, willy Ramos, pamela Krueger, frank delfino, Craig Meagher, tammy huang, yang shen, william olson, john Lin, eric smith. FlexBodies: Targeting intracellular tumor antigens with T cell redirecting bispecific antibodies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1084.
Abstract 110: Elevation of pro-apoptotic protein, PUMA, contributes to the growth suppression of lung cancer by platycodin D
Authors: Qing Wang, Hsin-Sheng Yang
Journal: Cancer Research (2022)

Abstract Lung cancer is the most devastating disease and leading cause of cancer death in men and women. Platycodin D is one of the major bioactive components of the Platycodon grandiflorum, a herb that is frequently used for the treatment of lung diseases in Chinese medicine. Platycodin D is a triterpenoid monomer with activities of antioxidant, anti-obesity, and anti-inflammatory. Studies have also shown that platycodin D has an anti-tumor effect on various types of cancer. However, the mechanism by which platycodin D suppresses tumorigenesis remains elusive and some experimental results are controversial. In this study, we aim to understand the effect of platycodin D on the growth of non-small lung cancer cells (NSCLC) and the underlying mechanism. We found that NSCLC cells (H1299, H2030, and A549 cells) treated with platycodin D significantly reduced the cell viability, decreased the number of colonies, impaired the mitochondrial function, and induced apoptosis. To understand the mechanism, the protein levels of the Bcl-2 protein family were examined and p53 upregulated modulator of apoptosis (PUMA) was found elevated by platycodin D treatment. The induction of PUMA expression by platycodin D treatment was through activation of the c-Jun N-terminal kinase (JNK) and AP-1 dependent transcription since JNK inhibitor or over-expression of dominant negative c-Jun abolished the elevated PUMA expression. Moreover, knockdown of JNK1, but not JNK2, significantly decreased the level of platycodin D-induced PUMA and cleaved caspase 3, indicating the essential role of JNK1 in platycodin D-induced apoptosis. Furthermore, platycodin D efficiently suppressed the tumor growth in the H1299 xenograft. Taken together, activation of JNK1 by platycodin D is essential for induction of apoptosis in suppression of growth of NSCLC, providing a new mechanism of how platylcodin D suppresses NSCLC. Citation Format: Qing Wang, Hsin-Sheng Yang. Elevation of pro-apoptotic protein, PUMA, contributes to the growth suppression of lung cancer by platycodin D [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 110.
Abstract 642: Spatial analysis of tumor infiltrating lymphocytes in histological images using deep learning predicts progression-free survival in colorectal cancer
Authors: Hongming Xu, Yoon Jin Cha, Jean Clemenceau, Jinhwan Choi, Sung Hak Lee, Jeonghyun Kang, Tae Hyun Hwang
Journal: Cancer Research (2022)

Abstract Histological distribution and density of tumor infiltrating lymphocytes (TILs) are known to be informative to cancer patients’ outcome. However, due to the heterogeneity and huge size of digitized pathology slides, it has been a challenging problem to quantify TILs-related features in whole slide images (WSI). This study aimed to explore the impact of spatial distribution of TILs quantified by deep learning (DL) approaches based on digitalized WSI stained with hematoxylin and eosin in patients with colorectal cancer (CRC). The cancer and TILs regions are first separately identified by deep learning models in the WSI. The TILs densities at tumor invasive margins are then quantified by image analysis algorithms and used for prognosis of progression-free survival (PFS) in CRC patients. The prognostic impact of spatial distributions of TILs in CRC patients was explored in the Yonsei cohort (n=180) and validated in the TCGA cohort (n=268). Two experienced pathologists manually measured TILs at the most invasive margin as 0-3 by the Klintrup-Mäkinen (KM) grading method and compared to DL approaches. On multivariate analysis, TILs densities within 200µm of the invasive margin (f_im200) was remained as the most significant prognostic factor for PFS (HR 0.004 [95% CI, 0.0001-0.1502], p=.002) in the Yonsei cohort. On multivariate analysis using the TCGA dataset, f_im200 retained prognostic significance for PFS (HR 0.031, [95% CI 0.001-0.645], p=.024). Inter-observer agreement of manual KM grading was insignificant in both cohorts. The survival analysis by pathologists’ manual KM grading showed statistically significant different PFS from the TCGA cohort, but not the Yonsei cohort. In summary, automated quantification of TILs at the invasive margin showed a prognostic utility to predict PFS, and could provide reproducible TILs density measurement in CRC patients. Citation Format: Hongming Xu, Yoon Jin Cha, Jean Clemenceau, Jinhwan Choi, Sung Hak Lee, Jeonghyun Kang, Tae Hyun Hwang. Spatial analysis of tumor infiltrating lymphocytes in histological images using deep learning predicts progression-free survival in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 642.
Abstract 2488: PET imaging of innate immunity activation <i>In Vivo</i> with redox-tuned 4-[18F]fluoro-1-naphthol
Authors: Seth T. Gammon, Federica Pisaneschi, Vincenzo Paolillo, Sarah Qureshy, David Piwnica-Worms
Journal: Cancer Research (2022)

Abstract High redox potential reactive oxygen and nitrogen species (ROS/RNS), such as O2 free radicals, superoxide, and hypochlorous acid, generated by activities of the NADPH oxidase-2 (NOX2)/myeloperoxidase (MPO) axis and related enzymes, are key effector molecules of innate immunity in physiological and diseased inflammatory states. Other lower energy species (H2O2, NO) provide adjuvant signaling functions. NOX2- and MPO-derived high energy radicals are known to oxidize naphthol species, wherein the naphthol products bind to proximate proteins and activated myeloid cells. Herein, we present 4-[18F]fluoro-1-naphthol ([18F]4FN), a novel redox-tuned radiopharmaceutical that selectively detects by positron emission tomography (PET) high energy radicals produced by activated innate immunity. The products of human MPO plus H2O2, but not H2O2 alone, rapidly and completely oxidized [18F]4FN. All-trans-retinoic acid-differentiated HL-60 "neutrophil-like" human cells activated with phorbol-12-myristate-13-acetate (PMA) retained [18F]4FN 5-fold over unstimulated cells. 4-ABAH, an MPO-specific inhibitor, or DPI, a broad oxidase inhibitor, blocked cellular retention by &amp;gt;95%. [18F]4FN PET/CT imaging readily discriminated foci of inflammation in vivo in three distinct murine models of acute inflammation: endotoxin-induced whole-body toxic shock, PMA-induced mild contact dermatitis of the ear, and lipopolysaccharide (LPS)-induced ankle arthritis. Mechanistically, in mice in vivo, 4-ABAH reduced inflammation-induced [18F]4FN retention, and Cybb-/- (Nox2-/-) gene-deletion strongly and significantly abrogated PMA-induced [18F]4FN retention. Thus, [18F]4FN shows promise as a robust redox-tuned reporter for imaging activation states of innate immunity by PET/CT, is ready for translation. [18F]4FN PET imaging may find application in a variety of inflammatory states associated with cancer therapy, immunotherapy-related adverse events, as well as other diseases, including arthritis, hepatitis, atherosclerosis, COVID-19, as well as up-staging and monitoring multi-organ inflammation. Citation Format: Seth T. Gammon, Federica Pisaneschi, Vincenzo Paolillo, Sarah Qureshy, David Piwnica-Worms. PET imaging of innate immunity activation In Vivo with redox-tuned 4-[18F]fluoro-1-naphthol [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2488.
Abstract 122: Hypoxia-reoxygenation couples enzyme and cofactor upregulation to quicken prostate cancer androgen biosynthesis and hormone therapy resistance
Authors: Liang Qin, Yoon-Mi Chung, Michael Berk, Bryan Naelitz, Eric Klein, Abhishek A Chakraborty, Nima Sharifi
Journal: Cancer Research (2022)

Abstract Androgen deprivation therapy depletes circulating testosterone and is the mainstay treatment for advanced prostate cancer by suppressing tumor androgen receptor signaling. Despite initial treatment response, castration-resistant prostate cancer nearly always develops and remains driven primarily by the androgen axis. We investigated how changes in oxygenation affect androgen synthesis. Our study indicates that when chronic hypoxia is coupled to reoxygenation, prostate cancer cells efficiently metabolize androgen precursors to produce androgens and activate AR. Hypoxia induces 3βHSD1, the rate-limiting androgen synthesis regulator, and reoxygenation replenishes necessary cofactors. Therefore, hypoxia and reoxygenation are both essential for potent androgen synthesis. The EGLN1/VHL/HIF2α pathway promoted transcription of HSD3B1 by directly binding the 5’ regulatory region of HSD3B1. HIF2α overexpression facilitated prostate cancer progression, which largely depends on 3βHSD1. PT2399, a specific HIF2α inhibitor, prevented prostate cancer cell proliferation. Our study indicates HIF2α is a potential therapeutic target in prostate cancer. Citation Format: Liang Qin, Yoon-Mi Chung, Michael Berk, Bryan Naelitz, Eric Klein, Abhishek A Chakraborty, Nima Sharifi. Hypoxia-reoxygenation couples enzyme and cofactor upregulation to quicken prostate cancer androgen biosynthesis and hormone therapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 122.